Tracking Git commits

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Core commits
RSS
Recent Commits to bioperl-live:master add primary_id as a constructor parameter Fix File::Path calls for older File::Path versions remove Id tags (strangely not removed from the last round more docs, for esummary more docs doc updates remove extraneous Cookie class add some synopsis info, remove TODO item (GET/POST is now implemented) clarify range throw, not croak Making return value of intersection consistent when one range is passed. Clarifying the conditions when union & intersection return an object. The use of $stop here is inconsistent, using $end. Merge branch 'circular' change exception on unknown moltype to debugging statement; at some point we can use this for validation, but until then it's a PITA w/o NCBI having a valid list of valid molecule types available ne, not != check for _instantiated-edness Add test and test data for InterPro parsing bug tiny change to Bio::FeatureIO::gff to allow the gmod chado gff3 bulk loader Merge branch 'master' of github.com:genehack/bioperl-live

Run commits
RSS
Recent Commits to bioperl-run:master StandaloneBlastPlus: don't automatically add ./ to remote database names [bug 2987] remove warning (patch courtesy Adam Witney Revert "add dots param" add dots param [RT 58464] patching to allow file names with spaces remove samtool cruft from MANIFEST small fixes, but the previous code does work when setting INFERNALDIR spelling move tests over to tempfile use (tmpdir not being cleaned up) move to tempfiles for cleanup algorithm can be SSEARCH as well; use test_output_file() for tempfile cleanup contigs off with Ubuntu packaged MAQ no_sequences -> num_sequences some tweaks to get rid of warnings more robust call to ulimit is(), not ok() skip if version greater than 1.2 (old primer3 code) add version() (backport from primer3redux) align left fix odd verbosity-dependent bug with EMBOSS tests

Ext commits
RSS
Recent Commits to bioperl-ext:master moved Bio::Tools::HMM and Bio::Ext::HMM into their own distro, got them compiling cleanly. tests not passing yet use UPPPER_TOL to catch the case when the expectation maximization step fixed Vitebi typo Fixed the typemap and also a memory bug in viterbi function in HMM.xs adding FEEDBACK:Support section to pod Bump to 1.007 (similar to trunk) ext patches (courtesy Thomas Jahns) get rid of some unended comment warnings from C compiler -fPIC needed for lib construction include errno definition removed DEBUG=1 IUPAC DNA support IUPAC DNA test case Add some helper code and tests to demo evalue oddities (bug 1857); casting issue? Add cast to correct pointer type (get rid of warnings) update version to last bioperl release bug 2329 bug 2074/2329 Removed Aaron's old test script (now in t/staden_read.t). Do we modify master ext makefile to account for this? bug 2074

Bioperl-DB (BioSQL)
RSS
Recent Commits to bioperl-db:master [RT 44466] remove corba-related scripts, now obsolete squash perl 5.12 warning ignore conf file add minimal .gitignore file weird duplication removed committing patch for bug #2958 test commit to check SVN::Notify Build.PL now checks for DBD drivers and attempts to DTRT remove MANIFEST.SKIP update Changes fix empty POD section some pod cleaning main trunk version is wrong * 02species.t now compared to similarly behaving instance, also creates comparable array [bug 2092] moved Bio into lib to make Module::Build installation more normal fixed up capitalisation; allowed --accept; improved script install; will install modules from lib fix up shebang lines so they can be converted during install remove Data::Dumper * scripts now convert over properly.